in progress

diff --git a/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java b/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java
index 22ddb1e..63db3b2 100644 (file)
--- a/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java
@@ -26,6 +26,7 @@
 
 package org.forester.surfacing;
 
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.SortedMap;
@@ -373,6 +374,68 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
         return sb;
     }
 
+    
+    
+    private StringBuffer getTaxonomyGroupDistribution( Phylogeny tol ) {
+        //TODO work on me    
+        
+        final SortedMap<String, SortedSet<String>> m = new TreeMap<String, SortedSet<String>>();
+        for( final Species species : getSpeciesData().keySet() ) {
+            for( final String combable_dom : getCombinableDomainIds( species ) ) {
+                if ( !m.containsKey( combable_dom ) ) {
+                    m.put( combable_dom, new TreeSet<String>() );
+                }
+                m.get( combable_dom ).add( species.getSpeciesId() );
+            }
+        }
+        Map<String,Integer> countz = new HashMap<String,Integer>();
+        for( final Map.Entry<String, SortedSet<String>> e : m.entrySet() ) {
+             for( final String tax_code : e.getValue() ) {
+             final String group = SurfacingUtil.obtainTaxonomyGroup( tax_code, tol );
+                if ( !ForesterUtil.isEmpty( group ) ) {
+                    if ( !countz.containsKey( group ) ) {
+                        countz.put( group, 1 );
+                    }
+                    else {
+                        countz.put( group, countz.get( group) + 1 );
+                    }
+                    
+                }
+                else {
+                    return null;
+                }
+                
+            }
+           
+        }
+        final StringBuffer sb = new StringBuffer();
+        
+        // i am just a template and need to be modified for "printout" TODO
+        for( final Map.Entry<String, SortedSet<String>> e : m.entrySet() ) {
+            sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + e.getKey() + "\">" + e.getKey() + "</a>" );
+            sb.append( ": " );
+            sb.append( "<span style=\"font-size:8px\">" );
+            for( final String tax : e.getValue() ) {
+                final String hex = SurfacingUtil.obtainHexColorStringDependingOnTaxonomyGroup( tax, null );
+                if ( !ForesterUtil.isEmpty( hex ) ) {
+                    sb.append( "<span style=\"color:" );
+                    sb.append( hex );
+                    sb.append( "\">" );
+                    sb.append( tax );
+                    sb.append( "</span>" );
+                }
+                else {
+                    sb.append( tax );
+                }
+                sb.append( " " );
+            }
+            sb.append( "</span>" );
+            sb.append( "<br>\n" );
+        }
+        return sb;
+    }
+    
+    
     private StringBuffer getSpeciesDataInAlphabeticalOrder( final boolean html,
                                                             final Map<String, Integer> tax_code_to_id_map,
                                                             final Phylogeny phy ) {

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index f23f865..f9fb313 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -101,6 +101,11 @@ public final class SurfacingUtil {
 
     public final static Pattern              PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
     private final static Map<String, String> _TAXCODE_HEXCOLORSTRING_MAP      = new HashMap<String, String>();
+  
+    
+    private final static Map<String, String> _TAXCODE_TAXGROUP_MAP = new HashMap<String, String>();
+    
+    
     private static final Comparator<Domain>  ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
 
                                                                                   @Override
@@ -1378,6 +1383,58 @@ public final class SurfacingUtil {
         }
         return _TAXCODE_HEXCOLORSTRING_MAP.get( tax_code );
     }
+    
+    
+    public static String obtainTaxonomyGroup( final String tax_code, final Phylogeny phy )
+            throws IllegalArgumentException {
+        if ( !_TAXCODE_TAXGROUP_MAP.containsKey( tax_code ) ) {
+            if ( ( phy != null ) && !phy.isEmpty() ) {
+                final List<PhylogenyNode> nodes = phy.getNodesViaTaxonomyCode( tax_code );
+                
+                if ( ( nodes == null ) || nodes.isEmpty() ) {
+                    throw new IllegalArgumentException( "code " + tax_code + " is not found" );
+                }
+                if ( nodes.size() != 1 ) {
+                    throw new IllegalArgumentException( "code " + tax_code + " is not unique" );
+                }
+                PhylogenyNode n = nodes.get( 0 );
+                String group = null;
+                Color c = null;
+                while ( n != null ) {
+                    if ( n.getNodeData().isHasTaxonomy()
+                            && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+                        c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getNodeData().getTaxonomy()
+                                .getScientificName(), tax_code );
+                        
+                        group = n.getNodeData().getTaxonomy()
+                                .getScientificName();
+                    }
+                    if ( ( c == null ) && !ForesterUtil.isEmpty( n.getName() ) ) {
+                        c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getName(), tax_code );
+                        group =  n.getName();
+                    }
+                    if ( c != null ) {
+                        break;
+                    }
+                    group = null;
+                    n = n.getParent();
+                }
+                if ( c == null ) {
+                    throw new IllegalArgumentException( "no group found for taxonomy code \"" + tax_code + "\"" );
+                }
+                
+                _TAXCODE_TAXGROUP_MAP.put( tax_code, group );
+            }
+            else {
+                throw new IllegalArgumentException( "unable to obtain group for code " + tax_code
+                        + " (tree is null or empty and code is not in map)" );
+            }
+        }
+        return _TAXCODE_TAXGROUP_MAP.get( tax_code );
+    }
+    
+    
+    
 
     public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
                                                           final SortedMap<String, Integer> domain_architecuture_counts,

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index a57974a..7391763 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -127,7 +127,7 @@ import org.forester.ws.wabi.TxSearch.TAX_RANK;
 @SuppressWarnings( "unused")
 public final class Test {
 
-    private final static boolean PERFORM_DB_TESTS          = false;
+    private final static boolean PERFORM_DB_TESTS          = true;
     private final static double  ZERO_DIFF                 = 1.0E-9;
     private final static String  PATH_TO_TEST_DATA         = System.getProperty( "user.dir" )
                                                                    + ForesterUtil.getFileSeparator() + "test_data"
@@ -501,7 +501,7 @@ public final class Test {
                 failed++;
             }
         }
-        ///////////////////////////////////////// System.exit( 0 );
+        System.exit( 0 );
         System.out.print( "UniProtKB id extraction: " );
         if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
             System.out.println( "OK." );
@@ -11503,14 +11503,14 @@ public final class Test {
                 System.out.println( entry4.getGeneName() );
                 return false;
             }
-            //            if ( !entry4.getChromosome().equals( "ras" ) ) {
-            //                System.out.println( entry4.getChromosome() );
-            //                return false;
-            //            }
-            //            if ( !entry4.getMap().equals( "ras" ) ) {
-            //                System.out.println( entry4.getMap() );
-            //                return false;
-            //            }
+            if ( !entry4.getChromosome().equals( "ras" ) ) {
+                System.out.println( entry4.getChromosome() );
+                return false;
+            }
+            if ( !entry4.getMap().equals( "ras" ) ) {
+                System.out.println( entry4.getMap() );
+                return false;
+            }
             //
             //TODO fails:
             //            final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" );

diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
index c65fb2a..29376bd 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
+++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
@@ -383,6 +383,15 @@ public final class SequenceDbWsTools {
                     seq.addCrossReference( x );
                 }
             }
+            if ( !ForesterUtil.isEmpty( db_entry.getChromosome() ) && !ForesterUtil.isEmpty( db_entry.getMap() ) ) {
+                seq.setLocation( "chr " + db_entry.getChromosome() + ", " + db_entry.getMap() );
+            }
+            else if ( !ForesterUtil.isEmpty( db_entry.getChromosome() ) ) {
+                seq.setLocation( "chr " + db_entry.getChromosome() );
+            }
+            else if ( !ForesterUtil.isEmpty( db_entry.getMap() ) ) {
+                seq.setLocation( db_entry.getMap() );
+            }
             final Taxonomy tax = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy() : new Taxonomy();
             if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) {
                 tax.setScientificName( db_entry.getTaxonomyScientificName() );